Human Gene GABRA6 (ENST00000274545.10_4) from GENCODE V47lift37
  Description: gamma-aminobutyric acid type A receptor subunit alpha6 (from RefSeq NM_000811.3)
Gencode Transcript: ENST00000274545.10_4
Gencode Gene: ENSG00000145863.11_10
Transcript (Including UTRs)
   Position: hg19 chr5:161,112,727-161,129,598 Size: 16,872 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr5:161,112,996-161,128,779 Size: 15,784 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:161,112,727-161,129,598)mRNA (may differ from genome)Protein (453 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: GBRA6_HUMAN
DESCRIPTION: RecName: Full=Gamma-aminobutyric acid receptor subunit alpha-6; AltName: Full=GABA(A) receptor subunit alpha-6; Flags: Precursor;
FUNCTION: GABA, the major inhibitory neurotransmitter in the vertebrate brain, mediates neuronal inhibition by binding to the GABA/benzodiazepine receptor and opening an integral chloride channel.
SUBUNIT: Binds UBQLN1 (By similarity). Generally pentameric. There are five types of GABA(A) receptor chains: alpha, beta, gamma, delta, and rho.
SUBCELLULAR LOCATION: Cell junction, synapse, postsynaptic cell membrane; Multi-pass membrane protein. Cell membrane; Multi-pass membrane protein.
SIMILARITY: Belongs to the ligand-gated ion channel (TC 1.A.9) family. Gamma-aminobutyric acid receptor (TC 1.A.9.5) subfamily. GABRA6 sub-subfamily.
WEB RESOURCE: Name=Protein Spotlight; Note=Forbidden fruit - Issue 56 of March 2005; URL="http://web.expasy.org/spotlight/back_issues/sptlt056.shtml";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: GABRA6
Diseases sorted by gene-association score: childhood absence epilepsy (7), neurotic disorder (5), epilepsy, generalized, with febrile seizures plus, type 5 (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 135.17 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 237.93 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -65.90269-0.245 Picture PostScript Text
3' UTR -173.20819-0.211 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR006028 - GABAA_rcpt
IPR001390 - GABAAa_rcpt
IPR005436 - GABBAa6_rcpt
IPR006202 - Neur_chan_lig-bd
IPR006201 - Neur_channel
IPR006029 - Neurotrans-gated_channel_TM
IPR018000 - Neurotransmitter_ion_chnl_CS

Pfam Domains:
PF02931 - Neurotransmitter-gated ion-channel ligand binding domain
PF02932 - Neurotransmitter-gated ion-channel transmembrane region

SCOP Domains:
63712 - Nicotinic receptor ligand binding domain-like
90112 - Neurotransmitter-gated ion-channel transmembrane pore

ModBase Predicted Comparative 3D Structure on Q16445
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0004890 GABA-A receptor activity
GO:0005216 ion channel activity
GO:0005230 extracellular ligand-gated ion channel activity
GO:0005254 chloride channel activity
GO:0008503 benzodiazepine receptor activity

Biological Process:
GO:0006811 ion transport
GO:0006821 chloride transport
GO:0007165 signal transduction
GO:0007214 gamma-aminobutyric acid signaling pathway
GO:0034220 ion transmembrane transport
GO:1902476 chloride transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0034707 chloride channel complex
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:1902711 GABA-A receptor complex


-  Descriptions from all associated GenBank mRNAs
  AK289461 - Homo sapiens cDNA FLJ77262 complete cds, highly similar to Homo sapiens gamma-aminobutyric acid (GABA) A receptor, alpha 6 (GABRA6), mRNA.
A28106 - Human GABAa receptor alpha-6 subunit.
BC096241 - Homo sapiens gamma-aminobutyric acid (GABA) A receptor, alpha 6, mRNA (cDNA clone MGC:116902 IMAGE:40005676), complete cds.
BC096242 - Homo sapiens gamma-aminobutyric acid (GABA) A receptor, alpha 6, mRNA (cDNA clone MGC:116905 IMAGE:40005680), complete cds.
BC099640 - Homo sapiens gamma-aminobutyric acid (GABA) A receptor, alpha 6, mRNA (cDNA clone MGC:116903 IMAGE:40005678), complete cds.
BC099641 - Homo sapiens gamma-aminobutyric acid (GABA) A receptor, alpha 6, mRNA (cDNA clone MGC:116904 IMAGE:40005679), complete cds.
S81944 - gamma-aminobutyric acid type A receptor alpha 6 subunit [human, cerebellum, mRNA Partial, 1732 nt].
KJ896848 - Synthetic construct Homo sapiens clone ccsbBroadEn_06242 GABRA6 gene, encodes complete protein.
KR711775 - Synthetic construct Homo sapiens clone CCSBHm_00030825 GABRA6 (GABRA6) mRNA, encodes complete protein.
AK090735 - Homo sapiens cDNA FLJ33416 fis, clone BRACE2019703, highly similar to Gamma-aminobutyric-acid receptor alpha-6 subunit precursor.
JD225049 - Sequence 206073 from Patent EP1572962.
JD203068 - Sequence 184092 from Patent EP1572962.
JD036346 - Sequence 17370 from Patent EP1572962.
JD238544 - Sequence 219568 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_flumazenilPathway - Cardiac Protection Against ROS
h_gabaPathway - Gamma-aminobutyric Acid Receptor Life Cycle

Reactome (by CSHL, EBI, and GO)

Protein Q16445 (Reactome details) participates in the following event(s):

R-HSA-8856398 NPTN binds GABA A receptors
R-HSA-975340 GABR heteropentamers:GABA transport Cl- from extracellular region to cytosol
R-HSA-112314 Neurotransmitter receptors and postsynaptic signal transmission
R-HSA-112315 Transmission across Chemical Synapses
R-HSA-977441 GABA A receptor activation
R-HSA-112316 Neuronal System
R-HSA-977443 GABA receptor activation

-  Other Names for This Gene
  Alternate Gene Symbols: A8K096, ENST00000274545.1, ENST00000274545.2, ENST00000274545.3, ENST00000274545.4, ENST00000274545.5, ENST00000274545.6, ENST00000274545.7, ENST00000274545.8, ENST00000274545.9, GBRA6_HUMAN, NM_000811, Q16445, Q4VAV2, uc317jfn.1, uc317jfn.2
UCSC ID: ENST00000274545.10_4
RefSeq Accession: NM_000811.3
Protein: Q16445 (aka GBRA6_HUMAN or GAA6_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.